PB

&pb namelist variables¶

Basic input options¶

ipb (Default = 2)

Option to set up a dielectric model for all numerical PB procedures. ipb = 1 corresponds to a classical geometric method, while a level-set based algebraic method is used when ipb > 2.

• 1: The dielectric interface between solvent and solute is built with a geometric approach. (ref.)
• 2: The dielectric interface is implemented with the level set function. Use of a level set function simplifies the calculation of the intersection points of the molecular surface and grid edges and leads to more stable numerical calculations. (ref.)
• 4: The dielectric interface is also implemented with the level set function. However, the linear equations on the grid points nearby the dielectric boundary are constructed using the IIM. In this option, The dielectric constant do not need to be smoothed, that is, smoothopt is useless. Only the linear PB equation is supported, that is, npbopt = 0. Starting from the Amber 2018 release, solvopt is no longer relevant as only one stable solver is supported. (ref.)
• 6: The dielectric interface is implemented analytically with the revised density function approach (sasopt = 2). The linear equations on the irregular points are constructed using the IIM and fully utilizing the analytical surface. Otherwise, it is exactly the same as ipb = 4. (ref.)
• 7: The dielectric interface is implemented analytically with the revised density function approach (sasopt = 2). The linear equations on the irregular points are constructed using the Χ-factor harmonic average method. (ref.)
• 8: The dielectric interface is implemented analytically with the revised density function approach (sasopt = 2). The linear equations on the irregular points are constructed using the secondorder harmonic average method. (ref.)

inp (Default = 1)

Option to select different methods to compute non-polar solvation free energy.

• 1: The total non-polar solvation free energy is modeled as a single term linearly proportional to the solvent accessible surface area (ref.). When using inp = 1:

  • sprob is reset to 1.4
  • cavity_surften is reset to 0.005
  • cavity_offset is reset to 0.000

• 2: The total non-polar solvation free energy is modeled as two terms: the cavity term and the dispersion term. The dispersion term is computed with a surface-based integration method (ref.) closely related to the PCM solvent for quantum chemical programs. (ref.) Under this framework, the cavity term is still computed as a term linearly proportional to the molecular solvent-accessible-surface area (SASA) or the molecular volume enclosed by SASA.

Keep in mind

Sometimes, high values for the solvation energy are obtained using inp=2. Check this section to see a workaround.

sander_apbs (Default = 0)

Option to use APBS for PB calculation instead of the built-in PBSA solver. This will work only through the iAPBS interface built into sander.APBS. Instructions for this can be found online at the iAPBS/APBS websites.

• 0: Don’t use APBS
• 1: Use sander.APBS

Options to define the physical constants¶

indi (Default = 1.0)

Internal dielectric constant. This corresponds to epsin in pbsa.

exdi (Default = 80.0)

External dielectric constant. This corresponds to epsout in pbsa.

emem (Default = 4.0)

Sets the membrane dielectric constant. Only used if memopt > 0, does nothing otherwise. Value used should be between indi and exdi or there may be errors. This corresponds to epsmem in pbsa.

smoothopt (Default = 1)

Instructs PB how to set up dielectric values for finite-difference grid edges that are located across the solute/solvent dielectric boundary.

• 0: The dielectric constants of the boundary grid edges are always set to the equal-weight harmonic average of indi and exdi.
• 1: A weighted harmonic average of indi and exdi is used for boundary grid edges. The weights for indi and exdi are fractions of the boundary grid edges that are inside or outside the solute surface. (ref.)
• 2: The dielectric constants of the boundary grid edges are set to either indi or exdi depending on whether the midpoints of the grid edges are inside or outside the solute surface.

istrng (Default = 0.0)

Ionic strength in Molarity (M). It is converted to mM for PBSA and kept as M for APBS.

radiopt (Default = 1)

The option to set up atomic radii.

• 0: Use radii from the prmtop file for both the PB calculation and for the non-polar calculation (see inp)
• 1: Use atom-type/charge-based radii by Tan and Luo (ref.) for the PB calculation. Note that the radii are optimized for Amber atom types as in standard residues from the Amber database and should work fine for standard complexes such as protein-protein, protein-DNA. On the other hand, if a molecule in your system was built by antechamber, i.e., if GAFF atom types are used, or any other extrenal software, radii from the prmtop file should be used (radiopt = 0). Check this thread for more info.

prbrad (Default = 1.4)

Solvent probe radius (in Å). Allowed values are 1.4 and 1.6. This corresponds to dprob in pbsa.

iprob (Default = 2.0)

Mobile ion probe radius (in Å) for ion accessible surface used to define the Stern layer.

sasopt (Default = 0)

Option to determine which kind of molecular surfaces to be used in the Poisson-Boltzmann implicit solvent model.

• 0: Use the solvent excluded surface as implemented by (ref.)
• 1: Use the solvent accessible surface. Apparently, this reduces to the van der Waals surface when the prbrad is set to zero.
• 2: Use the smooth surface defined by a revised density function. (ref.) This must be combined with `ipb > 2.

arcres (Default = 0.25)

The arcres keyword gives the resolution (in Å) of dots used to represent solvent accessible arcs. More generally, arcres should be set to max(0.125 Å, 0.5h) (h is the grid spacing). (ref.)

Options for implicit membranes¶

memopt (Default = 0)

Option to turn the implicit membrane on and off. The membrane is implemented as a slab like region with a uniform or heterogeneous dielectric constant depth profile. Details of the implicit membrane setup can be found here.

• 0: No implicit membrane used.
• 1: Use a uniform membrane dielectric constant in a slab-like implicit membrane. (ref.)
• 2: Use a heterogeneous membrane dielectric constant in a slab-like implicit membrane. The dielectric constant varies with depth from a value of 1 in the membrane center to 80 at the membrane periphery. The dielectric constant depth profile was implemented using the PCHIP fitting. (ref.)
• 3: Use a heterogeneous membrane dielectric constant in a slab-like implicit membrane. The dielectric constant varies with depth from a value of 1 in the membrane center to 80 at the membrane periphery. The dielectric constant depth profile was implemented using the Spline fitting. (ref.)

Keep in mind

• Calculations for implicit membranes can be performed only with PB
• A sample input file is shown here
• A tutorial on binding free energy calculation for membrane proteins is available here
• Check this thread for more info on Parameters for Implicit Membranes

mprob (Default = 2.70)

Membrane probe radius (in Å). This is used to specify the highly different lipid molecule accessibility versus that of the water. (ref.)

mthick (Default = 40)

Membrane thickness (in Å). This is different from the previous default of 20 Å.

mctrdz (Default = 0.0)

Membrane center (in Å) in the z direction.

poretype (Default = 1)

Turn on and off the automatic depth-first search method to identify the pore. (ref.)

• 0: Do not turn on the pore searching algorithm.
• 1: Turn on the pore searching algorithm.

Options to select numerical procedures¶

npbopt (Default = 0)

Option to select the linear, or the full nonlinear PB equation.

• 0: Linear PB equation (LPBE) is solved
• 1: Nonlinear PB equation (NLPBE) is solved

Note

While the linear PB equation (see tutorial) will suffice for most calculations, the nonlinear PB equation (see tutorial) is recommended for highly charged systems. Parameters such as eneopt or cutnb should be adjusted accordingly when using the NLPBE. Check the following threads (T1 and T2) on how to proceed when using NLPBE. Last but not least, take into account that using NLPBE can significantly increase the calculation time required for PB calculation.

solvopt (Default = 1)

Option to select iterative solvers.

• 1 Modified ICCG or Periodic (PICCG) if bcopt = 10.
• 2 Geometric multigrid. A four-level v-cycle implementation is applied by default.
• 3 Conjugate gradient (Periodic version available under bcopt = 10). This option requires a large linit to converge.
• 4 SOR. This option requires a large linit to converge.
• 5 Adaptive SOR. This is only compatible with npbopt = 1. This option requires a large linit converge. (ref.)
• 6 Damped SOR. This is only compatible with npbopt = 1. This option requires a large linit to converge. (ref.)

accept (Default = 0.001)

Sets the iteration convergence criterion (relative to the initial residue).

linit (Default = 1000)

Sets the maximum number of iterations for the finite difference solvers. Note that linit has to be set to a much larger value, e.g. 10000, for the less efficient solvers, such as conjugate gradient and SOR, to converge. This corresponds to maxitn in pbsa.

fillratio (Default = 4.0)

The ratio between the longest dimension of the rectangular finite-difference grid and that of the solute. For macromolecules is fine to use 4, or a smaller value like 2. A default value of 4 is large enough to be used for a small solute, such as a ligand molecule. Using a smaller value for fillratio may cause part of the small solute to lie outside the finite-difference grid, causing the finite-difference solvers to fail.

scale (Default = 2.0)

Resolution of the Poisson Boltzmann grid. It is equal to the reciprocal of the grid spacing (space in pbsa).

nbuffer (Default = 0)

Sets how far away (in grid units) the boundary of the finite difference grid is away from the solute surface; i.e., automatically set to be at least a solvent probe or ion probe (diameter) away from the solute surface.

nfocus (Default = 2)

Set how many successive FD calculations will be used to perform an electrostatic focussing calculation on a molecule. When nfocus = 1, no focusing is used. It is recommended that nfocus = 1 when the multigrid solver is used.

fscale (Default = 8)

Set the ratio between the coarse and fine grid spacings in an electrostatic focussing calculation.

npbgrid (Default = 1)

Sets how often the finite-difference grid is regenerated.

Options to compute energy and forces¶

bcopt (Default = 5)

Boundary condition options.

• 1: Boundary grid potentials are set as zero, i.e. conductor. Total electrostatic potentials and energy are computed.
• 5: Computation of boundary grid potentials using all grid charges. Total electrostatic potentials and energy are computed.
• 6: Computation of boundary grid potentials using all grid charges. Reaction field potentials and energy are computed with the charge singularity free formalism. (ref.)
• 10: Periodic boundary condition is used. Total electrostatic potentials and energy are computed. Can be used with solvopt = 1, 2, 3, or 4 and ipb = 1 or 2. It should only be used on charge-neutral systems. If the system net charge is detected to be nonzero, it will be neutralized by applying a small neutralizing charge on each grid (i.e. a uniform plasma) before solving.

eneopt (Default = 2)

Option to compute total electrostatic energy and forces.

• 1: Compute total electrostatic energy and forces with the particle-particle particle-mesh (P3M) procedure outlined in Lu and Luo. (ref.) In doing so, energy term EPB in the output file is set to zero, while EEL includes both the reaction field energy and the Coulombic energy. The van der Waals energy is computed along with the particle-particle portion of the Coulombic energy. The electrostatic forces and dielectric boundary forces can also be computed. (ref.) This option requires a nonzero cutnb and bcopt = 5 for soluble proteins / bcopt = 10 for membrane proteins.
• 2: Use dielectric boundary surface charges to compute the reaction field energy. Both the Coulombic energy and the van der Waals energy are computed via summation of pairwise atomic interactions. Energy term EPB in the output file is the reaction field energy. EEL is the Coulombic energy.
• 3: Similar to the first option above, a P3M procedure is applied for both solvation and Coulombic energy and forces for larger systems.
• 4: Similar to the third option above, a P3M procedure for the full nonlinear PB equation is applied for both solvation and Coulombic energy and forces for larger systems. A more robust and clean set of routines were used for the P3M and dielectric surface force calculations.

frcopt (Default = 0)

Option to compute and output electrostatic forces to a file named force.dat in the working directory.

• 0: Do not compute or output atomic and total electrostatic forces.
• 1: Reaction field forces are computed by trilinear interpolation. Dielectric boundary forces are computed using the electric field on dielectric boundary. The forces are output in the unit of kcal/mol·Å.
• 2: Use dielectric boundary surface polarized charges to compute the reaction field forces and dielectric boundary forces (ref.) The forces are output in the unit of kcal/mol·Å.
• 3: Reaction field forces are computed using dielectric boundary polarized charge. Dielectric boundary forces are computed using the electric field on dielectric boundary. (ref.) The forces are output in kcal/mol·Å.

scalec (Default = 0)

Option to compute reaction field energy and forces.

• 0: Do not scale dielectric boundary surface charges before computing reaction field energy and forces.
• 1: Scale dielectric boundary surface charges using Gauss’s law before computing reaction field energy and forces.

cutfd (Default = 5.0)

Atom-based cutoff distance to remove short-range finite-difference interactions, and to add pairwise charge-based interactions. This is used for both energy and force calculations. See Eqn (20) in Lu and Luo. (ref.)

cutnb (Default = 0.0)

Atom-based cutoff distance for van der Waals interactions, and pairwise Coulombic interactions when eneopt = 2. When cutnb is set to the default value of 0, no cutoff will be used for van der Waals and Coulombic interactions, i.e., all pairwise interactions will be included. When eneopt = 1, this is the cutoff distance used for van der Waals interactions only. The particle-particle portion of the Coulombic interactions is computed with the cutoff of cutfd._

nsnba (Default = 1)

Sets how often (steps) atom-based pairlist is generated.

Options to select a non-polar solvation treatment¶

decompopt (Default = 2)

Option to select different decomposition schemes when inp = 2. See (ref.) for a detailed discussion of the different schemes. The σ decomposition scheme is the best of the three schemes studied. (ref.) As discussed in (ref.), decompopt = 1 is not a very accurate approach even if it is more straightforward to understand the decomposition.

• 1: The 6/12 decomposition scheme.
• 2: The σ decomposition scheme.
• 3: The WCA decomposition scheme.

use_rmin (Default = 1)

The option to set up van der Waals radii. The default is to use van der Waals rmin to improve the agreement with TIP3P. (ref.)

• 0: Use atomic van der Waals σ values.
• 1: Use atomic van der Waals rmin values.

sprob (Default = 0.557)

Solvent probe radius (in Å) for solvent accessible surface area (SASA) used to compute the dispersion term, default to 0.557 Å in the σ decomposition scheme as optimized in (ref.) with respect to the TIP3P solvent and the PME treatment. Recommended values for other decomposition schemes can be found in Table 4 of (ref.). If use_sav = 0 (see below), sprob can be used to compute SASA for the cavity term as well. Unfortunately, the recommended value is different from that used in the dispersion term calculation as documented in (ref.). Thus, two separate calculations are needed when use_sav = 0, one for the dispersion term and one for the cavity term. Therefore, please carefully read (ref.) before proceeding with the option of use_sav = 0. Note that sprob was used for ALL three terms of solvation free energies, i.e., electrostatic, attractive, and repulsive terms in previous releases in Amber. However, it was found in the more recent study (ref.) that it was impossible to use the same probe radii for all three terms after each term was calibrated and validated with respect to the TIP3P solvent. (ref.)

vprob (Default = 1.300)

Solvent probe radius (in Å) for molecular volume (the volume enclosed by SASA) used to compute non-polar cavity solvation free energy, default to 1.300 Å, the value optimized in (ref.) with respect to the TIP3P solvent. Recommended values for other decomposition schemes can be found in Tables 1-3 of (ref.).

rhow_effect (Default = 1.129)

Effective water density used in the non-polar dispersion term calculation, default to 1.129 for decompopt = 2, the σ scheme. This was optimized in (ref.) with respect to the TIP3P solvent in PME. Optimized values for other decomposition schemes can be found in Table 4 of (ref.).

use_sav (Default = 1)

The option to use molecular volume (the volume enclosed by SASA) or to use molecular surface (SASA) for cavity term calculation. Recent study shows that the molecular volume approach transfers better from small training molecules to biomacromolecules.

• 0: Use SASA to estimate cavity free energy
• 1: Use the molecular volume enclosed by SASA

cavity_surften (Default = 0.0378)

The regression coefficient for the linear relation between the total non-polar solvation free energy (inp = 1), or the cavity free energy (inp = 2) and SASA/volume enclosed by SASA. The default value is for inp = 2 and set to the best of three tested schemes as reported in (ref.), i.e. decompopt = 2, use_rmin = 1, and use_sav = 1. See recommended values in Tables 1-3 for other schemes.

cavity_offset (Default = -0.5692)

The regression offset for the linear relation between the total non-polar solvation free energy (inp= 1), or the cavity free energy (inp = 2) and SASA/volume enclosed by SASA. The default value is for inp = 2 and set to the best of three tested schemes as reported in (ref.), i.e. decompopt = 2, use_rmin = 1, and use_sav = 1. See recommended values in Tables 1-3 for other schemes.

maxsph (Default = 400)

Approximate number of dots to represent the maximum atomic solvent accessible surface. These dots are first checked against covalently bonded atoms to see whether any of the dots are buried. The exposed dots from the first step are then checked against a non-bonded pair list with a cutoff distance of 9 Å to see whether any of the exposed dots from the first step are buried. The exposed dots of each atom after the second step then represent the solvent accessible portion of the atom and are used to compute the SASA of the atom. The molecular SASA is simply a summation of the atomic SASA’s. A molecular SASA is used for both PB dielectric map assignment and for NP calculations.

maxarcdot (Default = 1500)

Number of dots used to store arc dots per atom.

Options for output¶

npbverb (Default = 0)

Verbose mode.

• 0: Off
• 1: On